Search for Variation information by Variation ID:
Detailed information for vg0603161820:
| Variant ID: vg0603161820 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 3161820 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 340. )
Flanking Sequence (100 bp) in Reference Genome:
GAGATAGCTAAGCACCTGCCTGGTAGAACAGAAAACTCCATCAAGAATCACTGGAATGCAACAAAGAGAAGGCAATTCGCACGGAGGAGGAGCCGCGCTA[G/A]
CTCCAAGAACCCCAAATCTGGAACCCTTCTGCAAAACTACATCAAGAGCCTTGGAATTGGTCCAATCAAGTCAAGTGTTCGTCAAGCTCCACCAGAATCT
Reverse complement sequence
AGATTCTGGTGGAGCTTGACGAACACTTGACTTGATTGGACCAATTCCAAGGCTCTTGATGTAGTTTTGCAGAAGGGTTCCAGATTTGGGGTTCTTGGAG[C/T]
TAGCGCGGCTCCTCCTCCGTGCGAATTGCCTTCTCTTTGTTGCATTCCAGTGATTCTTGATGGAGTTTTCTGTTCTACCAGGCAGGTGCTTAGCTATCTC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.50% | 1.50% | 0.97% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 92.60% | 4.60% | 2.84% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 87.70% | 8.20% | 4.04% | 0.00% | NA |
| Tropical Japonica | 504 | 98.20% | 0.00% | 1.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.30% | 2.50% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 4.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0603161820 | G -> A | LOC_Os06g06740.1 | missense_variant ; p.Ser132Asn; MODERATE | nonsynonymous_codon ; S132N | Average:62.598; most accessible tissue: Callus, score: 88.334 | benign  |
1.386 |
TOLERATED | 0.40 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0603161820 | 2.12E-07 | 1.31E-12 | Awn_length | Jap_All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0603161820 | NA | 3.76E-06 | mr1062 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0603161820 | NA | 2.21E-06 | mr1062_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |